Your browser doesn't support javascript.
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.
Ramazzotti, Daniele; Angaroni, Fabrizio; Maspero, Davide; Gambacorti-Passerini, Carlo; Antoniotti, Marco; Graudenzi, Alex; Piazza, Rocco.
  • Ramazzotti D; Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Monza, Italy.
  • Angaroni F; Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy.
  • Maspero D; Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy.
  • Gambacorti-Passerini C; Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy.
  • Antoniotti M; Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Monza, Italy.
  • Graudenzi A; Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy.
  • Piazza R; Bicocca Bioinformatics, Biostatistics and Bioimaging Centre - B4, Milan, Italy.
Patterns (N Y) ; 2(3): 100212, 2021 Mar 12.
Article in English | MEDLINE | ID: covidwho-1051899
ABSTRACT
We introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which is an improvement on phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant profiles, also in conditions of sampling limitations. It then leverages variant frequency patterns to characterize the intra-host genomic diversity of samples, revealing undetected infection chains and pinpointing variants likely involved in homoplasies. On simulations, VERSO outperforms state-of-the-art tools for phylogenetic inference. Notably, the application to 6,726 amplicon and RNA sequencing samples refines the estimation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution, while co-occurrence patterns of minor variants unveil undetected infection paths, which are validated with contact tracing data. Finally, the analysis of SARS-CoV-2 mutational landscape uncovers a temporal increase of overall genomic diversity and highlights variants transiting from minor to clonal state and homoplastic variants, some of which fall on the spike gene. Available at https//github.com/BIMIB-DISCo/VERSO.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Variants Language: English Journal: Patterns (N Y) Year: 2021 Document Type: Article Affiliation country: J.patter.2021.100212

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Variants Language: English Journal: Patterns (N Y) Year: 2021 Document Type: Article Affiliation country: J.patter.2021.100212